2018年5月21日，Nature Reviews Molecular Cell Biology在线发表了中国科学院上海植物逆境生物学研究中心朱健康研究员、张惠明研究员与郎曌博研究员共同完成的题为“Dynamics and function of DNA methylation in plants”的综述文章。本博客将持续解读该文章，本文为连载第五期，包括第一章节DNA甲基化动态的最后一部分内容：DNA甲基化与去甲基化之间的动态平衡。

Dynamics and function of DNA methylation in plants

First author: Huiming Zhang; Affiliations: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences (中国科学院上海植物逆境生物学研究中心): Shanghai, China

Corresponding author: Jian- Kang Zhu

Coordination between DNA methylation and demethylation

ROS1 antagonizes RdDM to prevent DNA hypermethylation at specific loci, and ROS1 gene expression is reduced in all known RdDM mutants17,72,105-107. These observations revealed that DNA methylation and active demethylation activities are coordinated. A recent study of the A. thaliana DNA methylome showed that ROS1 activity counteracts RdDM at over 2,000 genomic regions. These regions were hypermethylated in ros1-4 mutant plants but not in double mutant ros1-4 and nrpd1-3 plants, which have defective functioning of both ROS1 and the largest subunit of POL IV, DNA-DIRECTED POL IV SUBUNIT 1 (NRPD1)98. The nrpd1-3 mutant displayed considerably lower levels of ROS1 gene expression and DNA hypermethylation in many genomic regions. Methylome analysis suggested that genomic hypermethylation in the nrpd1-3 mutant is at least partly due to suppressed ROS1 expression.

ROS1与RdDM相互拮抗预防特异位点上的DNA超甲基化，并且在所有已知的RdDM突变体中ROS1的表达量均降低。这说明DNA甲基化和主动去甲基化之间是相互协调的。最近一份关于拟南芥甲基化组的研究显示在超过2000个基因组区域上ROS1活性会抵消RdDM。这些区域在ros1-4突变体植株中被超甲基化，但在ROS1和POL IV最大亚基NRPD1同时功能缺失的ros1-4和nrpd1-3双突变体植株中并不会被超甲基化，nrpd1-3突变体的ROS1基因表达水平较低，并且很多基因组区域的DNA超甲基化水平也很低。甲基化组分析显示nrpd1-3突变体基因组超甲基化可能部分是由于ROS1基因表达被抑制所导致的。

In addition to RdDM mutants, met1 mutants also showed suppressed ROS1 gene expression108. The ROS1 gene promoter contains a 39 bp sequence in which methylation is decreased in met1 and RdDM mutants. Because hypomethylation in this particular sequence is accompanied by ROS1 gene repression, it appears that this sequence, termed the DNA methylation monitoring sequence (MEMS)106, may serve as a general indicator of RdDM and MET1 activities and may thus allow the coordination between DNA methylation and active DNA demethylation through transcriptional regulation of ROS1 (Fig. 2b). Consistent with this model, DNA hypermethylation of MEMS occurred in loss-of-function ros1 mutants, showing that MEMS is also targeted by ROS1106. The hypermethylation of MEMS in ros1 mutants is accompanied by increased ROS1 expression106. Upstream of MEMS, the ROS1 gene promoter contains a helitron transposon that may help attract DNA methylation factors and render the promoter responsive to DNA methylation. The specific transcription factors that promote ROS1 transcription by DNA methylation have not been identified.

除了RdDM突变体，met1突变体中ROS1基因表达同样被抑制。ROS1基因启动子含有一段39bp的序列，该序列在met1突变体和RdDM突变体中的甲基化程度均有所下降。因为这段序列的低甲基化伴随着ROS1基因的表达，因而这段叫做甲基化监测序列MEMS可能作为一个RdDM和MET1活性的指示器发挥作用，可能通过调控ROS1的转录来协调DNA甲基化和主动DNA去甲基化之间的平衡（图2b）。与该模型一致的是，MEMS的DNA超甲基化发生在ros1功能缺失突变体中，显示MEMS同样受到ROS1的靶定。MEMS在ros1突变体中的超甲基化伴随着ROS1基因表达量的增加。MEMS上游，即ROS1基因的启动子区域包含着一个helitron转座子，该转座子可能有利于吸引DNA甲基化因子，并且使得启动子响应于DNA甲基化。目前还未鉴定到能够通过DNA甲基化促进ROS1转录的特异性转录因子。

Like a thermostat that senses and maintains a stable temperature, MEMS can be considered as a ‘methylstat’ sequence that maintains homeostasis of ROS1-dependent DNA methylation levels in plant cells106,107. For instance, in met1-3 plants, in which ROS1 expression is considerably decreased, CG hypomethylation at 5S ribosomal DNA sequences is compensated by a progressive increase in CHH methylation levels in successive generations as a result of cumulative RdDM, eventually resulting in re-establishment of transcription silencing108. By contrast, decoupling ROS1 expression from regulation by RdDM causes widespread methylation loss and abnormal phenotypes that worsen progressively over generations109. Methylation- sensitive regulation of demethylase gene expression has also been observed in rice, maize and A. Lyrata107,110,111. Thus, this methylstat may be a conserved mechanism for regulating DNA methylation dynamics in plants. The methylstat mechanism may also exist in non-plant organisms with DNA methylation, including in mammalian cells, where it could help explain the genome-wide hypomethylation concurrent with locus-specific hypermethylation in cancer cells and in ageing humans112,113.

就像恒温器感知并维持一个稳定合适的温度，MEMS可以被看作为植物细胞中的一个“恒温器”序列能够维持ROS1依赖性DNA甲基化水平的内稳态。比如说，在met1-3突变体植株中，ROS1的表达显著降低，5S核糖体DNA序列上的CG低甲基化可以被连续世代所累积的RdDM而引起的CHH甲基化水平增加所弥补，最终重新建立起转录沉默。相反，解除ROS1表达与RdDM调控之间的关联会导致广泛的甲基化丢失和表型异常，并且随着世代的增加越来越严重。去甲基化酶基因表达的甲基化敏感调控同样在水稻、玉米和琴叶拟南芥中存在。因此，这种甲基化内稳态的调控方式在植物中是十分保守的。这种调控方式可能还存在于一些非植物物种中，包括一些哺乳动物细胞，其有助于解释癌症细胞中和老年人全基因范围上低甲基化与位点特异性超甲基化同时存在的现象。

doi: https://doi.org/10.1038/s41580-018-0016-z

Journal: Nature Reviews Molecular Cell Biology

Published date: 21 May, 2018